Plant Circular RNA Database

Detail information of AT3G11964_circ_g.6

			
						 General Information
					
						CircRNA Name
						AT3G11964_circ_g.6
					
						ID in PlantcircBase
						ath_circ_021148
					
						Alias
						3:3798014-3799641
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 3798014-3799641  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G11964						
					
						Parent gene annotation
						
							rRNA biogenesis protein RRP5
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G11964_circ_g.2 AT3G11964_circ_g.3 AT3G11964_circ_g.4 AT3G11964_circ_g.5 AT3G11964_circ_g.7 AT3G11964_circ_g.8 AT3G11964_circ_g.9 						
					
						Support reads
						1/1
					
						Tissues
						flower
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						AT3G11964.2:7
AT3G11964.1:7

General Information
CircRNA Name	AT3G11964_circ_g.6
ID in PlantcircBase	ath_circ_021148
Alias	3:3798014-3799641
Organism	Arabidpsis thaliana
Position	chr3: 3798014-3799641 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G11964
Parent gene annotation	rRNA biogenesis protein RRP5
Parent gene strand	-
Alternative splicing	AT3G11964_circ_g.2 AT3G11964_circ_g.3 AT3G11964_circ_g.4 AT3G11964_circ_g.5 AT3G11964_circ_g.7 AT3G11964_circ_g.8 AT3G11964_circ_g.9
Support reads	1/1
Tissues	flower
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	AT3G11964.2:7 AT3G11964.1:7

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TTTGTTCCTGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCTACAGTC
ACTTTTAGTAATATCAGATGATTGCAGGTCCGATATctttaagcattgcaggctttacagaaag
ctcccaaagttgagtctttttaatatcagtatgacacggctttgcaacaacccttgcagaaatt
gattgccc

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 874
Transcript exons: 3798014-3798161,3798264-3798338,3798439-3798592,3798834-
3798934,3799008-3799091,3799221-3799363,3799473-3799641
CTTTAAGCATTGCAGGCTTTACAGAAAGCTCCCAAAGTTGAGTCTTTTTAATATCAGTATGACA
CGGCTTTGCAACAACCCTTGCAGAAATTGATTGCCCAACTCTGAATTTGGCAAAAGGTTCATCA
CTTGTACTCGCATCATTTACCTCAGTTATGTGGATTCTCCCTCGGAAACTGTTGCCAAAGTTTA
CTCTAAGTTCAAAAGGCTTTATTTCAGTAATCTCGGCGTGGACAACAGAACCAACTTCACAGCT
GGATTTCTTCTTTGCCCTCTTAGAACGGGAAGTCTCAGAAGTGCCGGAAACAGAGTCAAGAAGT
AAAAGCAACCTCCCAGACGTTAAAGGGTTTTGCACAGCCTTAACAGAAGCAACAACACTTTGTC
CAGTGGAAAATTGTTTCACTGGCAACTTCTGAGTGTTATAGTCTGATACTGATGCATATCCTAT
AGTGTAACCATGCTCTGGAATCGACAAAACCAAGTGTTGCTCCTTCACAATCTCTACAACAGCA
CTGACCCTCTGGTGGACTTCAAGTTCCTTGGAGATTCCTCTTTTACGTTTCTTTTTTGAACTGT
TGGACACCTCTTTGGTTAAGTTGTTCAAGAGCTCAGGCCTCAAAGACAAATCAACTAGTCTCTC
TGCCCTAGATATATCAAGAACAACTGCATTGACAACAGAACCGGGTACCAAAGTAGCTCCACCC
ATATGATGCTGAGGTATAAAACCAAGGACGTTATTAATATTGTCAAAATTCACCACCACACCAA
GATCATTTTGTTCCTGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCT
ACAGTCACTTTTAGTAATATCAGATGATTGCAGGTCCGATAT
						
					

						Genomic sequence
						
							CTTTAAGCATTGCAGGCTTTACAGAAAGCTCCCAAAGTTGAGTCTTTTTAATATCAGTATGACA
CGGCTTTGCAACAACCCTTGCAGAAATTGATTGCCCAACTCTGAATTTGGCAAAAGGTTCATCA
CTTGTACTCGCATCATTTACCTATTCAATCCATAGTTGAGATATATAAGAAAATCTTCGTTCAC
CAAGTATTGAAGAACGAGTATTACAATCTAAAATGATGATGGTAAGCAACACAAGAACCTCAGT
TATGTGGATTCTCCCTCGGAAACTGTTGCCAAAGTTTACTCTAAGTTCAAAAGGCTTTATTTCA
GTAATCTGATAAGTATAAGCTGTTAGTATGAGGCAGCAGAAGTTATGGTGGCATAGACACAACT
AAAAAAAAAAAAAAGACTTAAGAAGGAAGGGCGATAGTAACCTCGGCGTGGACAACAGAACCAA
CTTCACAGCTGGATTTCTTCTTTGCCCTCTTAGAACGGGAAGTCTCAGAAGTGCCGGAAACAGA
GTCAAGAAGTAAAAGCAACCTCCCAGACGTTAAAGGGTTTTGCACAGCCTTAACAGAAGCAACA
ACACTGCCCATAGAAAATAATCAAAAAATACTTAGCTCCCATCAAGTAACTACAACAGTAAGGA
CAGCTATGTCTATTGCCAATAAAAGGTACAATGAGCTGCCAGTGGATGTATATACAAATTCAAA
TTTTATTAGTTTAGTTGGGCAGGGCAAAGAGTATATGGGAAATTAGGAACCATGACAAAGGGAA
GCAAATTAAATAAGTAAAAGATTGGCCAAAAATGGACGACTAGCAAGCTCACCTTTGTCCAGTG
GAAAATTGTTTCACTGGCAACTTCTGAGTGTTATAGTCTGATACTGATGCATATCCTATAGTGT
AACCATGCTCTGGAATCGACAAAACCTGGAAAAAAGGGCAGCTCTGAGTAACAATGTAACATGC
ACTAATTATCAACTTAATGCAATTATATACTTACCAAGTGTTGCTCCTTCACAATCTCTACAAC
AGCACTGACCCTCTGGTGGACTTCAAGTTCCTTGGAGATTCCTCTTTTACGTTTCTGGAGCAAG
ATAAAACACAACATGATATAAGCCGTAGCCCAATTTAGACTTATGCGAACCACGATGAGCATGG
GAGAAAACTTGAATAAAACAAAACTTTGCGAGAATATATCTTCTTAGAGTGAAACCTTTTTTGA
ACTGTTGGACACCTCTTTGGTTAAGTTGTTCAAGAGCTCAGGCCTCAAAGACAAATCAACTAGT
CTCTCTGCCCTAGATATATCAAGAACAACTGCATTGACAACAGAACCGGGTACCAAAGTAGCTC
CACCCACTACAAGAAGAAAACATAATGTATCAGACAAAGACTATGTAGAGATGTCTAAATCAGA
TGCAATCCATACGAAACTGTACCGAGAAACAGATTCTCCAAAATGACTTACTATGATGCTGAGG
TATAAAACCAAGGACGTTATTAATATTGTCAAAATTCACCACCACACCAAGATCATTTTGTTCC
TGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCTACAGTCACTTTTAG
TAATATCAGATGATTGCAGGTCCGATAT
						
					

			
		

Sequences
Splice junction sequence	TTTGTTCCTGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCTACAGTC ACTTTTAGTAATATCAGATGATTGCAGGTCCGATATctttaagcattgcaggctttacagaaag ctcccaaagttgagtctttttaatatcagtatgacacggctttgcaacaacccttgcagaaatt gattgccc
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 874 Transcript exons: 3798014-3798161,3798264-3798338,3798439-3798592,3798834- 3798934,3799008-3799091,3799221-3799363,3799473-3799641 CTTTAAGCATTGCAGGCTTTACAGAAAGCTCCCAAAGTTGAGTCTTTTTAATATCAGTATGACA CGGCTTTGCAACAACCCTTGCAGAAATTGATTGCCCAACTCTGAATTTGGCAAAAGGTTCATCA CTTGTACTCGCATCATTTACCTCAGTTATGTGGATTCTCCCTCGGAAACTGTTGCCAAAGTTTA CTCTAAGTTCAAAAGGCTTTATTTCAGTAATCTCGGCGTGGACAACAGAACCAACTTCACAGCT GGATTTCTTCTTTGCCCTCTTAGAACGGGAAGTCTCAGAAGTGCCGGAAACAGAGTCAAGAAGT AAAAGCAACCTCCCAGACGTTAAAGGGTTTTGCACAGCCTTAACAGAAGCAACAACACTTTGTC CAGTGGAAAATTGTTTCACTGGCAACTTCTGAGTGTTATAGTCTGATACTGATGCATATCCTAT AGTGTAACCATGCTCTGGAATCGACAAAACCAAGTGTTGCTCCTTCACAATCTCTACAACAGCA CTGACCCTCTGGTGGACTTCAAGTTCCTTGGAGATTCCTCTTTTACGTTTCTTTTTTGAACTGT TGGACACCTCTTTGGTTAAGTTGTTCAAGAGCTCAGGCCTCAAAGACAAATCAACTAGTCTCTC TGCCCTAGATATATCAAGAACAACTGCATTGACAACAGAACCGGGTACCAAAGTAGCTCCACCC ATATGATGCTGAGGTATAAAACCAAGGACGTTATTAATATTGTCAAAATTCACCACCACACCAA GATCATTTTGTTCCTGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCT ACAGTCACTTTTAGTAATATCAGATGATTGCAGGTCCGATAT
Genomic sequence	CTTTAAGCATTGCAGGCTTTACAGAAAGCTCCCAAAGTTGAGTCTTTTTAATATCAGTATGACA CGGCTTTGCAACAACCCTTGCAGAAATTGATTGCCCAACTCTGAATTTGGCAAAAGGTTCATCA CTTGTACTCGCATCATTTACCTATTCAATCCATAGTTGAGATATATAAGAAAATCTTCGTTCAC CAAGTATTGAAGAACGAGTATTACAATCTAAAATGATGATGGTAAGCAACACAAGAACCTCAGT TATGTGGATTCTCCCTCGGAAACTGTTGCCAAAGTTTACTCTAAGTTCAAAAGGCTTTATTTCA GTAATCTGATAAGTATAAGCTGTTAGTATGAGGCAGCAGAAGTTATGGTGGCATAGACACAACT AAAAAAAAAAAAAAGACTTAAGAAGGAAGGGCGATAGTAACCTCGGCGTGGACAACAGAACCAA CTTCACAGCTGGATTTCTTCTTTGCCCTCTTAGAACGGGAAGTCTCAGAAGTGCCGGAAACAGA GTCAAGAAGTAAAAGCAACCTCCCAGACGTTAAAGGGTTTTGCACAGCCTTAACAGAAGCAACA ACACTGCCCATAGAAAATAATCAAAAAATACTTAGCTCCCATCAAGTAACTACAACAGTAAGGA CAGCTATGTCTATTGCCAATAAAAGGTACAATGAGCTGCCAGTGGATGTATATACAAATTCAAA TTTTATTAGTTTAGTTGGGCAGGGCAAAGAGTATATGGGAAATTAGGAACCATGACAAAGGGAA GCAAATTAAATAAGTAAAAGATTGGCCAAAAATGGACGACTAGCAAGCTCACCTTTGTCCAGTG GAAAATTGTTTCACTGGCAACTTCTGAGTGTTATAGTCTGATACTGATGCATATCCTATAGTGT AACCATGCTCTGGAATCGACAAAACCTGGAAAAAAGGGCAGCTCTGAGTAACAATGTAACATGC ACTAATTATCAACTTAATGCAATTATATACTTACCAAGTGTTGCTCCTTCACAATCTCTACAAC AGCACTGACCCTCTGGTGGACTTCAAGTTCCTTGGAGATTCCTCTTTTACGTTTCTGGAGCAAG ATAAAACACAACATGATATAAGCCGTAGCCCAATTTAGACTTATGCGAACCACGATGAGCATGG GAGAAAACTTGAATAAAACAAAACTTTGCGAGAATATATCTTCTTAGAGTGAAACCTTTTTTGA ACTGTTGGACACCTCTTTGGTTAAGTTGTTCAAGAGCTCAGGCCTCAAAGACAAATCAACTAGT CTCTCTGCCCTAGATATATCAAGAACAACTGCATTGACAACAGAACCGGGTACCAAAGTAGCTC CACCCACTACAAGAAGAAAACATAATGTATCAGACAAAGACTATGTAGAGATGTCTAAATCAGA TGCAATCCATACGAAACTGTACCGAGAAACAGATTCTCCAAAATGACTTACTATGATGCTGAGG TATAAAACCAAGGACGTTATTAATATTGTCAAAATTCACCACCACACCAAGATCATTTTGTTCC TGTATGGTTCCCTTGATCAAACTCCCAATTGAGAATTTCTCAACCCAGCTACAGTCACTTTTAG TAATATCAGATGATTGCAGGTCCGATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.192550124

Conservation Information
Conserved circRNAs	NA
PMCS	0.192550124

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G11964_circ_g.6

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